This document explains the functionalities available in the a4Preproc package.
This package contains utility functions to pre-process data for the Automated Affymetrix Array Analysis suite of packages.
The feature annotation for a specific dataset, as required by the pipeline is extracted with the addGeneInfo function.
library(ALL)
data(ALL)
a4ALL <- addGeneInfo(eset = ALL)
print(head(fData(a4ALL)))## ENTREZID ENSEMBLID SYMBOL
## 1000_at 5595 ENSG00000102882 MAPK3
## 1001_at 7075 ENSG00000066056 TIE1
## 1002_f_at 1557 ENSG00000165841 CYP2C19
## 1003_s_at 643 ENSG00000160683 CXCR5
## 1004_at 643 ENSG00000160683 CXCR5
## 1005_at 1843 ENSG00000120129 DUSP1
## GENENAME
## 1000_at mitogen-activated protein kinase 3
## 1001_at tyrosine kinase with immunoglobulin like and EGF like domains 1
## 1002_f_at cytochrome P450 family 2 subfamily C member 19
## 1003_s_at C-X-C motif chemokine receptor 5
## 1004_at C-X-C motif chemokine receptor 5
## 1005_at dual specificity phosphatase 1print(head(featureData(a4ALL)))## An object of class 'AnnotatedDataFrame'
## featureNames: 1000_at 1001_at ... 1005_at (6 total)
## varLabels: ENTREZID ENSEMBLID SYMBOL GENENAME
## varMetadata: labelDescription## R version 4.2.0 RC (2022-04-19 r82224)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.15-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.15-bioc/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] hgu95av2.db_3.13.0 org.Hs.eg.db_3.15.0 AnnotationDbi_1.58.0
## [4] IRanges_2.30.0 S4Vectors_0.34.0 ALL_1.37.0
## [7] Biobase_2.56.0 BiocGenerics_0.42.0 a4Preproc_1.44.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.8.3 XVector_0.36.0 GenomeInfoDb_1.32.0
## [4] bslib_0.3.1 compiler_4.2.0 jquerylib_0.1.4
## [7] zlibbioc_1.42.0 bitops_1.0-7 tools_4.2.0
## [10] digest_0.6.29 bit_4.0.4 jsonlite_1.8.0
## [13] evaluate_0.15 RSQLite_2.2.12 memoise_2.0.1
## [16] pkgconfig_2.0.3 png_0.1-7 rlang_1.0.2
## [19] DBI_1.1.2 cli_3.3.0 yaml_2.3.5
## [22] xfun_0.30 fastmap_1.1.0 GenomeInfoDbData_1.2.8
## [25] stringr_1.4.0 httr_1.4.2 knitr_1.38
## [28] Biostrings_2.64.0 sass_0.4.1 vctrs_0.4.1
## [31] bit64_4.0.5 R6_2.5.1 rmarkdown_2.14
## [34] blob_1.2.3 magrittr_2.0.3 htmltools_0.5.2
## [37] KEGGREST_1.36.0 stringi_1.7.6 RCurl_1.98-1.6
## [40] cachem_1.0.6 crayon_1.5.1